knowledge extraction and semantic linking in the encyclopedia of life

Knowledge extraction and semantic linking in the

Encyclopedia of Life

Anne [email protected]

Performance Metrics

• 1631 URIs assigned to 487 text objects from 21 test species• 83% were correct• 20% of the text objects were not assigned a URI• 239 keys in the dictionary• Precision 0.89, Recall 1, F1 Score 0.942

Challenges and Errors

• Many ways to say the same thing– Uterine cannibalism = oophagy

• Negation (9%)• Describing related taxa (30%)• Word/phrase part (27%)• Generalities (15%)• Homonym (13%)

Finding Taxonomic Names

Challenges

Koko

Горилла

Guerilla

Eastern Lowland Gorilla

Gorilla graueri

Gorilla berengeiGorilla beringei

MatschieGorilla beringei mikenensisKing kong

Gorilla gorilla

Virunga

Gorila

Gorille

Mountain gorilla

大猩猩

ゴリラ

http://images.google.com.au/imgres?imgurl=http://www.namedevelopment.com/blog/archives/gorilla060606.png&imgrefurl=http://www.namedevelopment.com/blog/archives/2006/06/wanna_name_a_baby_gorilla.html&h=282&w=344&sz=195&hl=en&start=8&sig2=y2XXcY0mSVTDTYzxp9l06Q&um=1&tbnid=c4KRp2B-no4d1M:&tbnh=98&tbnw=120&ei=Q7tAR-WpK4mSeISCkcwK&prev=/images?q=gorilla&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://www.infovisual.info/02/img_en/075%20Morphology%20of%20a%20gorilla.jpg&imgrefurl=http://www.infovisual.info/02/075_en.html&h=357&w=581&sz=62&hl=en&start=22&sig2=nwDxePCqJeGL3vl5pnPRQA&um=1&tbnid=wsBLhJdEoRC-EM:&tbnh=82&tbnw=134&ei=X7tAR625NIeaeOze8M4K&prev=/images?q=gorilla&start=18&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://www.talkorigins.org/faqs/homs/gorilla.jpg&imgrefurl=http://www.talkorigins.org/faqs/homs/gorilla.html&h=321&w=511&sz=31&hl=en&start=41&sig2=fQiMt-zQX-4lefK1CZGXxA&um=1&tbnid=GFNIoe6HyOZ3kM:&tbnh=82&tbnw=131&ei=bbtAR8HCD4qMefSW0b8K&prev=/images?q=gorilla&start=36&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://www.infovisual.info/02/img_en/077%20Skeleton%20of%20a%20gorilla.jpg&imgrefurl=http://www.infovisual.info/02/077_en.html&h=334&w=386&sz=59&hl=en&start=69&sig2=oWb81JVca1I3nXJue55c8g&um=1&tbnid=FW5SJETmIJQiOM:&tbnh=106&tbnw=123&ei=f7tAR5K_CqXSeInhsNEK&prev=/images?q=gorilla&start=54&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://anthropologynet.files.wordpress.com/2007/08/chororapithecus-abyssinicus-gorilla-teeth-comparison.jpg&imgrefurl=http://anthropology.net/2007/08/24/c-abyssinicus-teeth-compared-to-modern-female-gorilla-jaw/&h=512&w=347&sz=50&hl=en&start=130&sig2=ZipP8NTiNJ8j4R1yyu14iA&um=1&tbnid=usaYbfcj8qwmJM:&tbnh=131&tbnw=89&ei=wLtAR_v-OqjGeLuPscwK&prev=/images?q=gorilla&start=126&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://www.skulls-skeletons.com/catalog/images/RS370-Gorilla,-Female.jpg&imgrefurl=http://www.skulls-skeletons.com/catalog/index.php?cPath=1_5_49&osCsid=71909ae8d&h=750&w=500&sz=22&hl=en&start=152&sig2=TwUie45pmXK1sXQ3dDPppA&um=1&tbnid=_Lg0CAxmUD-V6M:&tbnh=141&tbnw=94&ei=zrtAR-eGMY6QebvgsMEK&prev=/images?q=gorilla&start=144&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://photos.mongabay.com/06/1208gorilla0.jpg&imgrefurl=http://news.mongabay.com/2006/1207-gorillas.html&h=342&w=353&sz=30&hl=en&start=215&sig2=mtDrgdMRJ3-T8aONz7qwBQ&um=1&tbnid=8eiOL_wz3n5ciM:&tbnh=117&tbnw=121&ei=8rtAR9XVBKfyeKratL8K&prev=/images?q=gorilla&start=198&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://images.google.com.au/imgres?imgurl=http://marilynfenndesign.com/images/gorilla.jpg&imgrefurl=http://marilynfenndesign.com/illustration.html&h=450&w=300&sz=27&hl=en&start=261&sig2=lC-kk_9JETnyk8U2QEL5ng&um=1&tbnid=QDMjnvlsr140nM:&tbnh=127&tbnw=85&ei=KLxAR-uyBJ-MefHV1MAK&prev=/images?q=gorilla&start=252&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N

http://pin.primate.wisc.edu/fs/sheets/maps/gorilla_range_large.gif

http://en.wikipedia.org/wiki/Image:Primatenskelett-drawing.jpg

http://www.berggorilla.org/english/pic/wickings2b.gif

http://images.google.com.au/imgres?imgurl=http://personal.uncc.edu/jmarks/DNAHYB/Dna9.jpg&imgrefurl=http://personal.uncc.edu/jmarks/DNAHYB/dnahyb2.html&h=262&w=540&sz=17&hl=en&start=15&sig2=118s8Q5o3ScHKgItCmpW4Q&um=1&tbnid=x14udbAIYhI6MM:&tbnh=64&tbnw=132&ei=Yr9AR6DWEqLseb-lzcQK&prev=/images?q=gorilla+dna&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en

http://images.google.com.au/imgres?imgurl=http://www.nhm.ac.uk/about-us/news/2007/march/images/lice-gorilla-150_11098_1.jpg&imgrefurl=http://www.nhm.ac.uk/about-us/news/2007/march/news_11100.html&h=114&w=150&sz=10&hl=en&start=45&sig2=H6x-v95QzxejudcGacmGpw&um=1&tbnid=eKSpl4OlMwVgkM:&tbnh=73&tbnw=96&ei=jr9AR_2pHYy2eISPlb0K&prev=/images?q=gorilla+dna&start=36&ndsp=18&svnum=10&um=1&hl=en&safe=off&rls=GGLJ,GGLJ:2007-38,GGLJ:en&sa=N



















Challenges

Aotus trivirgatus Aotus Illiger 1811

Aotus Aotus Smith 1805 Aotus ericoides

.

Contextual data

PrimateMonkeyEyesFoodPanamaAotus nancymaae

Disambiguate by authority, species, contextual data

Contextual data

LegumePlant

FlowerMirbelieaAustralia

Aotus mollis

knowledge extraction and semantic linking in the encyclopedia of life

Technology

text objects

test species

oophagy negation

semantic linking

thing uterine cannibalism

related taxa

dictionary precision

knowledge extraction